Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Histone H2A.V .

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_3 g1647 g1647.t20 TTS g1647.t20 12286709 12286709
chr_3 g1647 g1647.t20 isoform g1647.t20 12287335 12288326
chr_3 g1647 g1647.t20 exon g1647.t20.exon1 12287335 12287520
chr_3 g1647 g1647.t20 cds g1647.t20.CDS1 12287335 12287520
chr_3 g1647 g1647.t20 exon g1647.t20.exon2 12287848 12287961
chr_3 g1647 g1647.t20 cds g1647.t20.CDS2 12287848 12287961
chr_3 g1647 g1647.t20 exon g1647.t20.exon3 12288081 12288326
chr_3 g1647 g1647.t20 cds g1647.t20.CDS3 12288081 12288212
chr_3 g1647 g1647.t20 TSS g1647.t20 12288402 12288402

Sequences

>g1647.t20 Gene=g1647 Length=546
ATGGTGAGAAAATGTTGATAACTGTGTCTTCTAACTTGAGCATACCGAAGAAAATCAAAT
ATAGTGCATTTAATACGATTTTCCTCGATTTTTATGAAAATATTCATAACCTGAATGCAA
AATCGAAGATTTTTTGTTAATGGCTTGTATTTTCTTGTTTTCTTAAAATTTCTAAACAAT
AGGCTGGAGGCAAAGCTGGAAAGGATTCAGGAAAAGCAAAGGCTAAGGCTGTCTCACGTT
CTGCACTTCCCAGTTGGACGTATCCACAGACATTTAAAGAACCGCACAACAAGTCATGGT
CGCGTCGGAGCAACCGCTGCTGTTTACTCTGCTGCTATCTTGGAATATTTGACTGCTGAA
GTTCTTGAGTTAGCTGGTAATGCATCAAAGGACTTGAAAGTCAAACGTATCACACCACGT
CATTTACAATTGGCCATTCGCGGAGATGAGGAACTCGATTCATTGATTAAAGCAACAATT
GCCGGTGGTGGTGTTATTCCTCATATTCACAAATCACTCATTGGCAAGAAAGGCGGTCCT
GAATAA

>g1647.t20 Gene=g1647 Length=143
MQNRRFFVNGLYFLVFLKFLNNRLEAKLERIQEKQRLRLSHVLHFPVGRIHRHLKNRTTS
HGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDSLIKA
TIAGGGVIPHIHKSLIGKKGGPE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g1647.t20 CDD cd00074 H2A 43 139 1.18339E-54
13 g1647.t20 Coils Coil Coil 14 37 -
12 g1647.t20 Gene3D G3DSA:1.10.20.10 Histone 23 143 5.2E-46
3 g1647.t20 PANTHER PTHR23430:SF280 HISTONE H2A.V 42 141 4.8E-62
4 g1647.t20 PANTHER PTHR23430 HISTONE H2A 42 141 4.8E-62
9 g1647.t20 PRINTS PR00620 Histone H2A signature 33 55 3.0E-34
7 g1647.t20 PRINTS PR00620 Histone H2A signature 63 78 3.0E-34
8 g1647.t20 PRINTS PR00620 Histone H2A signature 78 91 3.0E-34
6 g1647.t20 PRINTS PR00620 Histone H2A signature 92 106 3.0E-34
5 g1647.t20 PRINTS PR00620 Histone H2A signature 119 137 3.0E-34
2 g1647.t20 Pfam PF00125 Core histone H2A/H2B/H3/H4 27 111 1.6E-17
1 g1647.t20 Pfam PF16211 C-terminus of histone H2A 112 141 1.5E-12
15 g1647.t20 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 5 -
16 g1647.t20 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 6 24 -
14 g1647.t20 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 25 143 -
18 g1647.t20 SMART SM00414 h2a4 26 142 6.9E-60
10 g1647.t20 SUPERFAMILY SSF47113 Histone-fold 43 119 1.82E-34
11 g1647.t20 SignalP_EUK SignalP-noTM SignalP-noTM 1 26 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0003677 DNA binding MF
GO:0046982 protein heterodimerization activity MF
GO:0000786 nucleosome CC

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below. There were no conditions that were differentially expressed